sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / parsimony.h

diff --git a/parsimony.h b/parsimony.h
index 74ebefdc2d185eaa325a8ec4beff12fc04733cff..bf0e0d4f90198ef353c2c1899414f699454c8a7e 100644 (file)
--- a/parsimony.h
+++ b/parsimony.h
@@ -12,25 +12,31 @@
  */
 
 #include "treecalculator.h"
-#include "treemap.h"
-#include "globaldata.hpp"
+#include "counttable.h"
 
 /***********************************************************************/
 
 class Parsimony : public TreeCalculator  {
        
        public:
-               Parsimony(TreeMap* t) : tmap(t) {};
+               Parsimony() {};
                ~Parsimony() {};
-               EstOutput getValues(Tree*);
-               //EstOutput getValues(Tree*, string, string) { return data; }
+               EstOutput getValues(Tree*, int, string);
                
        private:
-               GlobalData* globaldata;
-               Tree* copyTree;
+               struct linePair {
+                       int start;
+                       int num;
+                       linePair(int i, int j) : start(i), num(j) {}
+               };
+               vector<linePair> lines;
+       
                EstOutput data;
-               TreeMap* tmap;
-               map<string, int>::iterator it;
+               int processors;
+               string outputDir;
+       
+               EstOutput driver(Tree*, vector< vector<string> >, int, int, CountTable*); 
+               EstOutput createProcesses(Tree*, vector< vector<string> >, CountTable*);
 };
 
 /***********************************************************************/